Are motherboard fan hookups necessary if the fans are already
connected to the powerlines going to the hard drives? The motherboard
hookups are for voltage/speed control and monitoring, or do they also
provide power? What is the proper way to hook up those fans?

Are motherboard fan hookups necessary if the fans are already
connected to the powerlines going to the hard drives?

Usually not necessary although there are mother boards that will not
work if the CPU fan is not hooked up to protect the CPU it is however
advisable since the motherboard hookups allow you to monitor speed and
allow the computer to speed up/slow down the fans depending on need

The motherboard hookups are for voltage/speed control and monitoring,
or do they also provide power?

They also provide power

What is the proper way to hook up those fans?

Usually it is a 2 wire hookup with a 'murphy' proof connector that can
only be connected one way

The motherboard hookups have a third wire for speed sensing, and if a
fan is not connected to the main cpu1 fan header on the motherboard,
many motherboards will not turn on. Other than that there is no reason
to use the motherboard fan headers. This is especially true for higher
powered fans. It is not unusal for large or fast fans to overwork the
small trace power lines that run to the motherboards fan headers. I
have seen many motherboards where the fan headers do not work
properly, so I prefer to use the atx style power connectors instead
when feasible.